Detailed information of TA system TA096074

Bioinformatically predicted

Overview

TA module

• Type: II
• Classification (family/domain): vapBC/VapC-VagC
• Location: 154506..155131
• Replicon: plasmid unnamed1
• Accession: NZ_CP026804
• Organism: Shigella flexneri strain 89-141

Toxin (Protein)

• Gene name: vapC
• Uniprot ID: Q6XVU6
• Locus tag: C1P88_RS24135
• Protein ID: WP_000911318.1
• Coordinates: 154733..155131 (+)
• Length: 133 a.a.

Antitoxin (Protein)

• Gene name: vapB
• Uniprot ID: Q7BEJ0
• Locus tag: C1P88_RS24130
• Protein ID: WP_000450531.1
• Coordinates: 154506..154733 (+)
• Length: 76 a.a.

Genomic Context

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
C1P88_RS24130	154506..154733	+	228	WP_000450531.1	toxin-antitoxin system antitoxin VapB	Antitoxin
C1P88_RS24135	154733..155131	+	399	WP_000911318.1	type II toxin-antitoxin system VapC family toxin	Toxin
C1P88_RS24140	155140..155319	-	180	Protein_182	hypothetical protein	-
C1P88_RS24145	155364..156520	+	1157	WP_134799775.1	IS3 family transposase	-
C1P88_RS24150	156565..157488	+	924	Protein_184	IS630 family transposase	-
C1P88_RS24155	157642..158586	-	945	WP_004996485.1	lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase	-
C1P88_RS24160	158651..159601	-	951	WP_004970430.1	virulence factor VirK	-

Associated MGEs

MGE detail	Similar MGEs	Relative position	MGE Type	Cargo ARG	Virulence gene	Coordinates	Length (bp)
	-	inside	Non-Mobilizable plasmid	-	spa24 / spa33 / spa32 / spa13 / spa47 / spa15 / mxiA / mxiA / mxiA / mxiA / mxiC / mxiC / mxiD / mxiD / mxiE / mxiM / mxiL / mxiN / mxiK / mxiJ / mxiI / mxiH / mxiG / ipgF / ipgE / ipgD / icsB / ipgA / ipgB1 / ipgC / ipaB / ipaC / ipaD / ipaA / ipaJ / ospC3 / ospC1 / ospD3/senA / ipaH4.5 / ipaH1.4 / ospE2 / ospE2 / ipaH2.5 / ipgB2 / ospD1 / ospF / ospD2 / ospC2 / ospC4 / ospC3 / ospB / icsP/sopA / nleE / ospC2 / ipaH7.8 / ospG / ipaH9.8 / ospI / papC / icsA/virG / icsA/virG / virA / spa40 / spa29 / spa9 / spa24 / spa33 / spa32 / spa13 / spa47 / spa15 / mxiA / mxiC / mxiD / mxiE / mxiM / mxiL / mxiN / mxiK / mxiJ / mxiI / mxiH / mxiG / mxiG / ipgF / ipgE / ipgD / ipgD / ipgD / ipgD / icsB / icsB / ipgA	1..245004	245004

Relative position:
(1) inside: TA loci is completely located inside the MGE;
(2) overlap: TA loci is partially overlapped with the MGE;
(3) flank: The TA loci is located in the 5 kb flanking regions of MGE.

Domains

Predicted by InterproScan

Toxin

• PIN domain (5-125)

Antitoxin

• SpoVT-AbrB domain (7-51)

Sequences

Toxin

Protein

• Length: 133 a.a.
• Molecular weight: 14845.09 Da
• Isoelectric Point: 8.5264

>T96074 WP_000911318.1 NZ_CP026804:154733-155131 [Shigella flexneri]
MLKFMLDTNICIFTIKNKPASVRERFNLNQGRMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHT
GQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS

Nucleotide

• Length: 399 bp

>T96074 NZ_CP026804:154733-155131 [Shigella flexneri]
ATGCTGAAGTTTATGCTCGATACCAACATCTGCATTTTTACGATAAAGAACAAACCCGCCAGCGTCAGGGAGCGTTTTAA
CCTGAACCAGGGGAGAATGTGTATCAGTTCGGTCACCCTGATGGAGCTGATATATGGTGCAGAAAAAAGCCAGATGCCTG
AACGTAATCTCGCTGTGATCGAGGGATTTGTTTCCCGCATTGATGTTCTGGATTACGACGCTGCTGCAGCCACACACACC
GGCCAGATAAGAGCAGAACTTGCCCGTCAGGGACGCCCTGTCGGGCCATTTGATCAAATGATCGCAGGTCATGCCCGCAG
TCGGGGGCTGATTATTGTGACTAATAACACCCGGGAATTTGAACGTGTGGGCGGCCTGAGAACTGAAGACTGGAGCTGA

Antitoxin

Protein

• Length: 76 a.a.
• Molecular weight: 8565.62 Da
• Isoelectric Point: 4.7513

>AT96074 WP_000450531.1 NZ_CP026804:154506-154733 [Shigella flexneri]
METTVFLSNRSQAVRLPKAVALPENVKRVEVIAVGRTRIITPAGETWDEWFDGHSVSTDFMDNREQPGMQERESF

Nucleotide

• Length: 228 bp

>AT96074 NZ_CP026804:154506-154733 [Shigella flexneri]
ATGGAAACCACCGTATTTCTCAGCAACCGCAGCCAGGCGGTCAGACTGCCAAAAGCGGTTGCATTGCCGGAAAACGTAAA
ACGCGTTGAAGTGATTGCTGTCGGACGAACCAGAATCATTACGCCAGCCGGAGAGACATGGGACGAATGGTTCGACGGAC
ACAGCGTCAGCACCGATTTTATGGATAACAGGGAACAGCCCGGCATGCAGGAAAGGGAGTCATTCTGA

Structures

Toxin

• PDB: 6SD6

Antitoxin

• PDB: 3TND
• AlphaFold DB: Q7BEJ0